Hi Luigi
Try
set.seed(1)
PLATE <-
data.frame(Delta.Rn = rnorm(500),
Cycle = rnorm(500),
Delta2 = rnorm(500)+1,
Well = rep(1:50, each = 10))
head(PLATE,10)
xyplot(Delta.Rn+Delta2 ~ Cycle | Well,
data = subset(PLATE, Well %in% 1:49),
allow.multiple = TRUE,
ylab="Fluorescence (Delta Rn)",
xlab="Cycles",
main="TITLE",
scales = list(
x = list(draw = FALSE),
y = list(draw = FALSE),
relation="same",
alternating=TRUE),
as.table = TRUE,
layout = c(10,5),
par.settings = list(
strip.background=list(col="white"),
# layout.heights = list(strip = 0.8),
axis.text = list(cex = 0.6),
par.xlab.text = list(cex = 0.75),
par.ylab.text = list(cex = 0.75),
par.main.text = list(cex = 0.8),
superpose.symbol = list(pch = ".", cex = 2,
col = c(2,4) )
),
strip = FALSE,
type = "p",
key = list(text = list(label = c("Delta.Rn","Delta2")),
points = list(cex = 0.6, pch = 16, col = c(2,4)),
cex = 0.6,
x = 0.9,
y = 0.1),
panel = panel.superpose,
panel.groups = function(x,y,...){
panel.xyplot(x,y,... )
# text argument can be a vector of values not
# necessarily the group name
pnl = panel.number() # needed as group.number if added is now either 1 or 2
grid.text(c(LETTERS,letters)[pnl],
y = 0.93, x = 0.5,
default.units = "npc",
just = c("left", "bottom"),
gp = gpar(fontsize = 7) )
}
)
Remember to delete the group argument (I forgot to at first as the groups are now Delta.Rn Delta2)
You may have 1+ empty panels so put the legend there where ever it is just amend the x and y or fine tune them
you can have the pch = "." and increase cex but it will become as square with large cex
Duncan
-----Original Message-----
From: Luigi Marongiu [mailto:marongiu.luigi at gmail.com]
Sent: Thursday, 23 April 2015 10:05
To: Duncan Mackay
Subject: Re: [R] high density plots using lattice dotplot()
Dear Duncan,
sorry to come back so soon, but i wanted to ask you whether it would
be possible to plot two sets of lines within each box, let's say a
main value A and a secondary value B. In normal plots I could use a
plot() followed by points(); what would be the strategy here?
Thank you again,
best regards,
Luigi
On Wed, Apr 22, 2015 at 6:46 AM, Duncan Mackay <dulcalma at bigpond.com> wrote:
Hi Luigi
I should have made up an example to make things easier when I replied today
This should get you going
set.seed(1)
PLATE <-
data.frame(Delta.Rn = rnorm(500),
Cycle = rnorm(500),
Well = rep(1:50, each = 10))
head(PLATE)
xyplot(Delta.Rn ~ Cycle | Well,
data = PLATE,
groups = Well,
ylab="Fluorescence (Delta Rn)",
xlab="Cycles",
main="TITLE",
scales = list(
x = list(draw = FALSE),
y = list(draw = FALSE),
relation="same",
alternating=TRUE),
as.table = TRUE,
layout = c(10,5),
par.settings = list(
strip.background=list(col="white"),
# layout.heights = list(strip = 0.8),
axis.text = list(cex = 0.6),
par.xlab.text = list(cex = 0.75),
par.ylab.text = list(cex = 0.75),
par.main.text = list(cex = 0.8)
superpose.symbol = list(pch = ".", cex = 2)
),
strip = FALSE,
type = "p",
col = 1,
panel = panel.superpose,
panel.groups = function(x,y,...,group.number){
panel.xyplot(x,y,... )
# text argument can be a vector of values not
# necessarily the group name
grid.text(c(LETTERS,letters)[group.number],
y = 0.93, x = 0.5,
default.units = "npc",
just = c("left", "bottom"),
gp = gpar(fontsize = 7) )
}
)
You could use panel.text instead of grid.text
Duncan
-----Original Message-----
From: Luigi Marongiu [mailto:marongiu.luigi at gmail.com]
Sent: Wednesday, 22 April 2015 08:24
To: Duncan Mackay
Subject: Re: [R] high density plots using lattice dotplot()
Dear Duncan,
thank you for your reply. I tried to implement your suggestions but as
is on your reply did not work (actually R crashed) and a slight
elaboration returned the figure attached, which is essentially still
displaying text and not drawing the data. Here is what I wrote:
xyplot(Delta.Rn ~ Cycle | Well,
data = PLATE,
ylab="Fluorescence (Delta Rn)",
xlab="Cycles",
main=TITLE,
scales = list(
x = list(draw = FALSE),
y = list(draw = FALSE),
relation="same",
alternating=TRUE),
as.table = TRUE,
layout = c(24,16),
par.settings = list(
strip.background=list(col="white"),
axis.text = list(cex = 0.6),
par.xlab.text = list(cex = 0.75),
par.ylab.text = list(cex = 0.75),
superpose.symbol = list(pch = ".", cex = 2)
),
strip = FALSE,
type = "p",
layout.heights = list(strip = 0.8),
panel = function(x,y, subscripts, groups,...){
panel.superpose(x,y,subscripts,groups,...,
col = ...)
panel.text(x,y,...,cex = 0.6)
}
)
How can I improve the script?
Many thanks
Luigi
On Tue, Apr 21, 2015 at 12:35 AM, Duncan Mackay <dulcalma at bigpond.com> wrote:
Hi Luigi
Strips take up space so if you are willing to not have strip and put the
strip values within the plot area then
xyplot(y ~ x|cond.factor, data = ...,
as.table = T,
groups = ...,
layout = ...,
drop.unused = T,
par.settings = list(axis.text = list(cex = 0.6),
par.xlab.text = list(cex = 0.75),
par.ylab.text = list(cex = 0.75)
superpose.symbol = list(pch = ".", cex = 2)
),
strip = FALSE,
scales = list(x = list(alternating = 2),
y = list(alternating = FALSE)
),
type = "p",
panel = function(x,y, subscripts, groups,...){
panel.superpose(x,y,subscripts,groups,...,
col = ...)
panel.text(x,y,...,cex = 0.6)
}
)
if the text values are a vector
stext = ...
xyplot(y ~ x|cond.factor, data = ...,
as.table = T,
groups = ...,
layout = ...,
drop.unused = T,
par.settings = list(axis.text = list(cex = 0.6),
par.xlab.text = list(cex = 0.75),
par.ylab.text = list(cex = 0.75)
superpose.symbol = list(pch = ".", cex = 2)
),
strip = FALSE,
scales = list(x = list(alternating = 2),
y = list(alternating = FALSE)
),
type = "p",
panel = function(x,y, subscripts, groups,...){
pnl = panel.number()
panel.superpose(x,y,subscripts,groups,...,
col = ...)
panel.text(x,y,stext[pnl],cex = 0.6)
}
)
you could also you group.number instead of pnl if it is needed elsewhere.
text position could be done in a similar fashion if needed to be in
different places for some panels.
If you require the strip then an additional par.settings is
layout.heights = list(strip = 0.8)
or even untested in this situation
strip = FALSE
strip.left = TRUE
Regards
Duncan
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
Armidale NSW 2351
Email: home: mackay at northnet.com.au
-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Luigi
Marongiu
Sent: Sunday, 19 April 2015 19:28
To: r-help
Subject: [R] high density plots using lattice dotplot()
Dear all,
I am trying to plot the results of a PCR experiments that involves 384
individual plots. Admittedly the space for the plots will be tiny, but
I just nedd some icon to have a feeling of the layout of the
experiment and a quick comparison of the plots.
I believe that lattice would be the right tool, but when I tried to
implement i got an error. Specifically the output would be a A4 pdf,
so with about 600 cm2 of drawing space, which gives about 1.5 cm2 for
each plot; removing the labels that might just work.
So I have the y values = 'fluorescence', x 'values' = cycles and 384
'well' data. I implemented to begin with:
xyplot(fluorescence ~ cycles | well,
ylab="Fluorescence",
xlab="Cycles",
main=list(draw = FALSE),
scales = list(
x = list(draw = FALSE),
y = list(draw = FALSE),
relation="same",
alternating=TRUE),
layout = c(24,16),
par.settings = list(strip.background=list(col="white")),
pch = "."
)
but the the individual graphs show only the writing "data" instead of
the actual plots.
How can I overcome this error?
Thank you
Best regards
Luigi
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